Filtering protein models by fuzzy restraints

The example file set
of low-resolution docking decoys was obtained by a
docking with GRAMM {Vakser 1995} of a TruA enzyme structure (PDB code
1VS3, apo form) to its tRNA substrate (PDB code 2V0G, a complex with an
unrelated protein). As a reference we used the native structure of this
complex (PDB code 2NR0; Figure 1). We produced 30000 decoys with the grid step =
3.5 , and repulsion parameter = 20. The grid-step radius was used as a
projection of an atom. The systematic search through the rotational
coordinates was performed every 10 degree.
While original published file set contained 30k decoys and had to be splittedintothree parts
due to system limitations, we encourage you to try a shorter example of 100 decoys.

For discrimination of native-like complexes with FILTREST3D we used six
distance restraints. First, we chose protein residues R50 and N52 known
to be involved in catalysis of isomerization of U39 in tRNA and
introduced two specific amino acid-nucleotide restraints. Second, we
identified additional putative RNA-binding residues (R23, H119, R162.)
that were both predicted as RNA-binding by the PPRINT webserver (Figure 2A) and were located in regions of positive
electrostatic potential (Figure 2B), as calculated
with the APBS tool with the PyMol program {DeLano 2002} for performing
electrostatic calculations. For these four residues we defined a general
restraint for interactions with any nucleotide of the whole tRNA molecule.

We filled Filtrest3D’s server form and ran
a filtering process. After one minute the result
for 100 testing decoys appeared.

As visible in the output 2 decoys satisfy
restraints completely. They the RMSD to the native structure of 22.36 Å and
26.56 Å. They are similar to each other and can be considered native-like
(Figure 3).

Figure 2: The analysis of the protein surface of TruA. A – Regions,
which according to PPRINT server could interact with RNA are colored
yellow. B – Electrostatic map of the protein surface. The positive
charged regions are blue, while negative charged regions are red.

Figure 3: A,B – Each of two best scored decoys, which were found by
Filtrest3D superimposed on the reference structure of complex. Only
proteins are superimposed. Reference structure is colored in blue
tones, while decoys are colored in red tones. All atoms, which were
used to make restraints have VDW representation. Cα of marked amino
acids are colored white, while O3’ atoms of nucleic acids are yellow. C
– Two best scored decoys. Proteins are superimposed.